SAXSdb — 4pkf

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

TutD

Thauera aromatica

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	TutG × 2 （O68396） TutF × 2 （O68394） GLYCEROL × 6 CHLORIDE ION × 2 IRON/SULFUR CLUSTER × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O68395_THAAR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–864； UniProt 1–864

TutG

Thauera aromatica

UniProt O68396

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	TutD × 2 （O68395） TutF × 2 （O68394） GLYCEROL × 6 CHLORIDE ION × 2 IRON/SULFUR CLUSTER × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O68396_THAAR
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–81； UniProt 1–81

TutF

Thauera aromatica

UniProt O68394

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	TutD × 2 （O68395） TutG × 2 （O68396） GLYCEROL × 6 CHLORIDE ION × 2 IRON/SULFUR CLUSTER × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O68394_THAAR
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–60； UniProt 1–60

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4pkf
Deposition date deposition_date	2014-05-14
Structure title title	Benzylsuccinate synthase alpha-beta-gamma complex
Keywords keywords	radical, complex, LYASE; LYASE
Experimental Method method	X-RAY DIFFRACTION

▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

4pkf__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4pkf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4pkf__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	42.28 Å
Rg (electron density)	42.23 Å
Total Rg	42.47 Å
Atom count	15404
Residues	1926
Excluded volume	272320 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4pkf__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	TutD
Molecular weight formula_weight	99117.1 kDa
EC 编号 ec_number	4.1.99.11
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	8580

MNDIVSAKVLEYKGKKLNFTPEDPAEETIPADELHEHLQKPSTARTKRLKERCRWKHASAGEFIEKSVTAGIERMRYLTEAHKASEGKPEAIRRALGLANVLNKSTLVLQEDEFIVGYHAEDPNMFPLYPELSHMAVQDYLRSDYSPQPADEAAAINEYWKPHSLQSKCQPYFDPADLGRMYQVSSMEAPSFASGYNSIVPPYETVLEDGLLARIKLAEKHIAEAQADMSTFPWNGTKGLDNIAKIDNWKAMVIACKAVISWARRQGRLCKIVAENFETDPKRQAELLEIADICQRIPAEPCKGLKDAMQAKFFTFLICHAIERYASGYAQKEDTLLWPYYKASVVDKKFQPMSHMDAVELVEMERLKISEHGAGKSRAYREIFPGSNDLFILTVGGTNAKGEDACNDMTDAILEAAKRIRTAEPSIVFRYSKKNREKTLRWVFECIRDGLGYPSIKHDEIGTEQMKEYAKFSLNGNGATDEEAHNWVNVLCMSPGIHGRRKTQKTRSEGGGSIFPAKLLEISLNDGYDWSYADMQLGPKTGDLSSLKSFEDVWEAFRKQYQYAINLCISTKDVSRYFEQRFLQMPFVSAIDDGCMELGMDACALSEQPNGWHNPITTIVAANSLVAIKKLVFEEKKYTLEQLSQALKANWEGFEEMRVDFKRAPKWGNDDDYADGIITRFYEEIIGGEMRKITNYSGGPVMPTGQAVGLYMEVGSRTGPTPDGRFGGEAADDGGISPYMGTDKKGPTAVLRSVSKVQKNQKGNLLNQRLSVPIMRSKHGFEIWNSYIKTWHDLNIDHVQFNVVSTDEMRAAQREPEKHHDLIVRVSGYSARFVDIPTYGQNTIIARQEQDFSASDLEFLNVEISGTGSGSSHHHHHH

Source Source

Source organism organism	Thauera aromatica
NCBI taxonomy ID ncbi_taxonomy_id	59405
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	TutG
Molecular weight formula_weight	9303.3 kDa
EC 编号 ec_number	4.1.99.11
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MEGSNMETGQNLQNQPHTEVGTARPCRSCKWQTPDPTDPHRGQCTANRHAMGGVWKRWLRDVENTTCSRHEEGKLSFRDHV

Source Source

Source organism organism	Thauera aromatica
NCBI taxonomy ID ncbi_taxonomy_id	59405
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	TutF
Molecular weight formula_weight	6865.7 kDa
EC 编号 ec_number	4.1.99.11
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MGTTTCKQCANFFPVPKDADDYEAGKADCVREKEDEKGKYWLSKPIFENSAQCEAFQTKR

Source Source

Source organism organism	Thauera aromatica
NCBI taxonomy ID ncbi_taxonomy_id	59405
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	836

▼

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	4pkfB00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	490 — High-Potential Iron-Sulfur Protein; Chain A
Homologous superfamily homologous superfamily	20 —

▶

Unit-cell length a length_a	113.424 Å
Unit-cell length b length_b	120.421 Å
Unit-cell length c length_c	136.048 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.002 Å
Low-resolution limit resolution_low	49.532 Å
R factor r_factor	0.1313
R_work r_work	0.1288
R_free r_free	0.1770

Benzylsuccinate synthase alpha-beta-gamma complex

1. Protein Identity and Related Structures Protein Identity & Related Structures

TutD

State in the Current Structure

Other States of the Same Protein in the Database

TutG

State in the Current Structure

Other States of the Same Protein in the Database

TutF

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4pkf__assembly_1__model_1

4pkf__assembly_1__model_1 | I(q)

4pkf__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Benzylsuccinate synthase alpha-beta-gamma complex

1. Protein Identity and Related Structures Protein Identity & Related Structures

TutD

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

TutG

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

TutF

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4pkf__assembly_1__model_1

4pkf__assembly_1__model_1 | I(q)

4pkf__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)